to cram functionality is in the making
Added an example with gzip compression
added directionality checking in callsam and fixed it for when the reference assembly is given
Merge branch 'master' of ssh://git.code.sf.net/p/callsam/code
Fixed forward reverse reads a bit
forward and reverse reads must now be present to produce high quality SNP calls.  Also refactored the code a bit and fixed the error that it was only counting forward reads and making everything low quality.
fixed variant calling bug where upper case and lower case were being considered as two different nts
Fixed a problem with deletions followed by new reads, but it is just a band-aid
Removed the rewind message that makes no sense to users
changing it so that there is a non-threaded version which is less buggy
back to single thread and hopefully working
back to single thread and hopefully working
fixed some syntax bug